Introduction to Cytoscape and it’s Apps - Session 1a

Part A: Network Analysis with Cytoscape

Goals and Motivations

By the end of these sessions you should be able to:

• Understand the major applications of network biology
• Find relevant networks and pathways
• Import your data into Cytoscape
• Perform basic topological and other network analyses
• Master network layouts and data visualization
• Know where to find relevant Cytoscape apps and tutorials
• Be able to analyze scRNA-seq data using Cytoscape - Only resource provided.

Introduction to Network Biology

Why Networks?

Networks are everywhere… especially in biology!

• Molecular networks
• Understand the major applications of network biology
• Find relevant networks and pathways
• Cell-cell communication
• Nervous systems
• Social networks

Transcriptomics

• In the early days:

• Then came microarrays:

• And now, the network view:

Single Cell Transcriptomics

Proteomics

Networks are powerful tools…

• Reduce complexity
• More efficient than tables
• Great for data integration
• Intuitive visualization

Advantages of Networks as Tool

Analysis

• Topological properties
• Hubs and subnetworks
• Classify, cluster and diffuse
• Data integration

Visualization

• Data overlays
• Layouts and animation
• Exploratory analysis
• Context and interpretation

Applications in Research

(Click Here for more network examples:)

Biological Network Taxonomy

Pathways

• Metabolic
• Signaling
• Regulatory
• Disease

Interactions

Similarity

We will now go to the next session (1 B) to understand terms about public repositories.